I would say you should be able to get adequate compaction using only the clay to back fill around your drain pipe. I would make some sort of anti-seep collar just to be on the safe side and since you are already there.
The muck from the bottom would surely be good for your garden, but a soil test would also help determine if you need lime and fertilizer to add with it, this is normal anyway. When you dig the muck you will see the color difference immediately and know the previously excavated depth when you reach it.
As far as how dry the bottom will get, it depends on how much water is coming in and the weather, lots of dry weather will equal dryer conditions, and the more rain, obviously the reverse is true. How deep are you shooting for? The dry season is getting a bit short, but a 40 x 80 excavation isn't a hard to manage size and would be easy to complete in a couple days or less with an excavator and dump truck, providing your haul is short and you don't have any problems. The money is hard to swallow at first, but the first time you sit next to your pond and watch the ripples onthe surface you won't think about the money, just how glad you are that you spent it.
I haven't seen your pond, but I advise anyone against taking heavy equipment into an unknown bottom like that without a larger machine and rigging around to recover it, should you become, sorry, I mean when you become mired, because you will if you are getting any work done.
